Mileage would help, along with a detailed history of how it ran, then what happened after repairs, etc.
Having said that, has he checked out the glow system? Even with a bad plug or two, the car would start up but perhaps run like doo. It's a quick check, and doesn't cost a dime to do. THe procedure is outlined in TDIclub under TDI 101 FAQ.
Next, disconnect the temperature sensor on the engine (also covered in the GLow-Plugs 101 in TDIClub). If the car starts right up and runs fine with the sensor disconnected, then the temp sensor is bad.
Next, I'd check the N75 if he has't checked that yet. You can test it with an ohmeter. I'm not sure of the value for the resistance, but on the 1.8t, it's like 35 ohms. If resitance is infinite, or zero, then the N75 valve is bad. They go bad frequently, and it controls the boost to the turbo electronically.
You can also test it manually. Disconnect the vacuum hose to the wastegate, connect a hand-vacuum pump to the wastegate, and pump up the pressure as high as it will go. Then start the car. If it runs fine, then you know that your N75 is not creating vaccum to keep the waste-gate open and it should be replaced. If the hand-vacuum pump does not register any vacuum at all when applied to the wastegate, then your wastegate is bad, and needs to be replaced.
When he had the intercooler hoses off, id he check for breaks/splits, etc. That will cause you to lose boost.
Who did the timing belt? Did he do it, or a sketchy shop. Perhaps the injection pump is off a tooth. It can happen given the amount of play in the lock pin on the 1998 TDI.
If all of the above check out and do not solve your problem, then I'd say that you have a mechanical problem. Have the injectors pop-tested. If they check out, then look to the injection pump. So long as the shop did not drop crud into the intake ports when they cleaned the intake, I doubt there are problems with air getting to the motor. The intake manifold clogs up due to a bend in the pipe where the goo collects. I've seen really gummed up intakes, that still had pretty clean intake ports on the head: enough to let it run fine.
Good luck